Added base classes for object types, vocabulary types, collection types, and property types

Moved definitions to datamodel

Author: JosePizarro3

bam_data_store/datamodel/__init__.py

@@ -0,0 +1,314 @@
+import re
+from enum import Enum
+from typing import Any, Optional
+
+from pydantic import BaseModel, Field, field_validator, model_validator
+
+
+class DataType(str, Enum):
+    BOOLEAN = 'BOOLEAN'
+    CONTROLLEDVOCABULARY = 'CONTROLLEDVOCABULARY'
+    DATE = 'DATE'
+    HYPERLINK = 'HYPERLINK'
+    INTEGER = 'INTEGER'
+    MATERIAL = 'MATERIAL'
+    MULTILINE_VARCHAR = 'MULTILINE_VARCHAR'
+    OBJECT = 'OBJECT'
+    REAL = 'REAL'
+    TIMESTAMP = 'TIMESTAMP'
+    VARCHAR = 'VARCHAR'
+    XML = 'XML'
+
+
+class EntityDef(BaseModel):
+    """
+    Abstract base class for all masterdata entity definitions. The entity definitions are immutable properties.
+    This class provides a common interface (with common attributes like `version`, `code` and
+    `description`.) for all entity definitions.
+    """
+
+    version: int = Field(
+        ...,
+        description="""
+        Version of the entity definition. This is an integer that is incremented each time the
+        definition is changed.
+        """,
+    )  # ? is this useful?
+
+    code: str = Field(
+        ...,
+        description="""
+        Code string identifying the entity with an openBIS inventory definition. Must be
+        uppercase and separated by underscores, e.g. `'EXPERIMENTAL_STEP'`.
+        """,
+    )
+
+    description: str = Field(
+        ...,
+        description="""
+        Description of the entity. This is the human-readable text for the object and must be
+        as complete and concise as possible. The German description can be added after the English
+        description separated by a double slash (//), e.g. `'Chemical Substance//Chemische Substanz'`.
+        """,
+    )
+
+    # TODO check ontology_id, ontology_version, ontology_annotation_id, internal (found in the openBIS docu)
+
+    @field_validator('code')
+    @classmethod
+    def validate_code(cls, value: str) -> str:
+        if not value or not re.match(r'^[A-Z_]+$', value):
+            raise ValueError('`code` must be uppercase and separated by underscores')
+        return value
+
+
+class BaseObjectTypeDef(EntityDef):
+    """
+    Definition class used for the common fields for `CollectionTypeDef`, `ObjectTypeDef`, and `DataSetType`.
+    It adds the fields of `validation_script`.
+    """
+
+    validation_script: Optional[str] = Field(
+        default=None,
+        description="""
+        Script written in Jython used to validate the object type.
+        """,
+    )  # ? is this truly used?
+
+
+class CollectionTypeDef(BaseObjectTypeDef):
+    """
+    Definition class for a collection type. E.g.:
+
+    ```python
+    class DefaultExperiment(BaseModel):
+        defs = CollectionTypeDef(
+            version=1,
+            code='DEFAULT_EXPERIMENT',
+            description='',
+            validation_script='DEFAULT_EXPERIMENT.date_range_validation',
+        )
+    ```
+    """
+
+    pass
+
+
+class DataSetTypeDef(BaseObjectTypeDef):
+    """
+    Definition class for a data set type. E.g.:
+
+    ```python
+    class RawData(BaseModel):
+        defs = DataSetTypeDef(
+            version=1,
+            code='RAW_DATA',
+            description='',
+        )
+    """
+
+    # TODO check descriptions
+
+    main_dataset_pattern: Optional[str] = Field(
+        default=None,
+        description="""""",
+    )
+
+    main_dataset_path: Optional[str] = Field(
+        default=None,
+        description="""""",
+    )
+
+
+class ObjectTypeDef(BaseObjectTypeDef):
+    """
+    Definition class for an object type. It adds the fields of `generated_code_prefix`, `auto_generated_codes`,
+    and `validation_script` to the common attributes of an entity definition. E.g.:
+
+    ```python
+    class Instrument(BaseModel):
+        defs = ObjectTypeDef(
+            version=1,
+            code='INSTRUMENT',
+            description='
+            Measuring Instrument//Messger\u00e4t
+            ',
+            generated_code_prefix='INS',
+        )
+    ```
+    """
+
+    generated_code_prefix: Optional[str] = Field(
+        default=None,
+        description="""
+        A short prefix for the defined object type, e.g. 'CHEM'. If not specified, it is defined
+        using the first 3 characters of `code`.
+        """,
+    )
+
+    auto_generated_codes: bool = Field(
+        True,
+        description="""
+        Boolean used to generate codes using `generated_code_prefix` and a unique number. Set to
+        True by default.
+        """,
+    )
+
+    @model_validator(mode='after')
+    @classmethod
+    def model_validator_after_init(cls, data: Any) -> Any:
+        """
+        Validate the model after instantiation of the class.
+
+        Args:
+            data (Any): The data containing the fields values to validate.
+
+        Returns:
+            Any: The data with the validated fields.
+        """
+        if not data.generated_code_prefix:
+            data.generated_code_prefix = data.code[:3]
+        return data
+
+
+class PropertyTypeDef(EntityDef):
+    """
+    Definition class for a property type. It adds the fields of `property_label`, `data_type`,
+    `vocabulary_code`, `metadata`, `dynamic_script`, and `multivalued` to the common attributes of
+    an entity definition. E.g.:
+
+    ```python
+    class Alias(PropertyTypeDef):
+        defs = PropertyTypeDef(
+            version=1,
+            code='ALIAS',
+            description='
+            e.g. abbreviation or nickname//z.B. Abkürzung oder Spitzname//z.B. Abkürzung oder Spitzname
+            ',
+            data_type='VARCHAR',
+            property_label='Alternative name',
+        )
+    ```
+    """
+
+    property_label: str = Field(
+        ...,
+        description="""
+        Label that appears in the inventory view. This is the human-readable text for the property
+        type definition, and it typically coincides with the `code`, e.g., `'Monitoring date'` for the
+        `MONITORING_DATE` property type.
+        """,
+    )
+
+    data_type: DataType = Field(
+        ...,
+        description="""
+        The data type of the property, i.e., if it is an integer, float, string, etc. The allowed
+        data types in openBIS are:
+            - `BOOLEAN`
+            - `CONTROLLEDVOCABULARY`
+            - `DATE`
+            - `HYPERLINK`
+            - `INTEGER`
+            - `MATERIAL`
+            - `MULTILINE_VARCHAR`
+            - `OBJECT`
+            - `REAL`
+            - `TIMESTAMP`
+            - `VARCHAR`
+            - `XML`
+
+        These are defined as an enumeration in the `DataType` class.
+
+        Read more in https://openbis.readthedocs.io/en/latest/uncategorized/register-master-data-via-the-admin-interface.html#data-types-available-in-openbis.
+        """,
+    )
+
+    vocabulary_code: Optional[str] = Field(
+        default=None,
+        description="""
+        String identifying the controlled vocabulary used for the data type of the property. This is
+        thus only relevant if `data_type == 'CONTROLLEDVOCABULARY'`.
+        """,
+    )
+
+    metadata: Optional[dict] = Field(
+        default=None,
+        description="""""",
+    )
+
+    dynamic_script: Optional[str] = Field(
+        default=None,
+        description="""""",
+    )
+
+    multivalued: Optional[str] = Field(
+        default=None,
+        description="""""",
+    )
+
+
+class PropertyTypeAssignment(PropertyTypeDef):
+    """
+    aaa
+    """
+
+    mandatory: bool = Field(
+        ...,
+        description="""
+        If `True`, the property is mandatory and has to be set during instantiation of the object type.
+        If `False`, the property is optional.
+        """,
+    )
+
+    show_in_edit_views: bool = Field(
+        ...,
+        description="""
+        If `True`, the property is shown in the edit views of the ELN in the object type instantiation.
+        If `False`, the property is hidden.
+        """,
+    )
+
+    section: str = Field(
+        ...,
+        description="""
+        Section to which the property type belongs to. E.g., `'General Information'`.
+        """,
+    )
+
+    unique: Optional[str] = Field(
+        default=None,
+        description="""""",
+    )
+
+    internal_assignment: Optional[str] = Field(
+        default=None,
+        description="""""",
+    )
+
+
+class VocabularyTypeDef(EntityDef):
+    """
+    Definition class for a vocabulary type. E.g.:
+    """
+
+    url_template: Optional[str] = Field(
+        default=None,
+        description="""""",
+    )
+
+
+class VocabularyTerm(VocabularyTypeDef):
+    """
+    aaa
+    """
+
+    label: str = Field(
+        ...,
+        description="""""",
+    )
+
+    official: bool = Field(
+        True,
+        description="""""",
+    )